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Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture.

Yin LM, Jiang GH, Wang Y, Wang Y, Liu YY, Jin WR, Xu YD, Zhang QH, Yang YQ - J. Biomed. Sci. (2009)

Bottom Line: By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC).Totally 3 same KEGG pathways were found among the three groups.Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China. collegeylm@hotmail.com

ABSTRACT

Background: Asthma has become an important public health issue and approximately 300 million people have suffered from the disease worldwide. Nowadays, the use of acupuncture in asthma is increasing. This study intended to systematically analyze and compare the gene expression profiles between the asthmatic and acupuncture-treated asthmatic rat lung, and tried to gain insight into the molecular mechanism underlying the early airway response (EAR) phase of asthma treated by acupuncture.

Methods: Four tag libraries of serial analysis of gene expression (SAGE) were established from lung tissues of control rats (CK), asthmatic rats (AS), asthmatic rats treated by acupuncture (ASAC), and control rats treated by acupuncture (CKAC). Bioinformatic analyses were carried out by using the methods including unsupervised hierarchical clustering, functional annotation tool of the database for annotation, visualization, and integrated discovery (DAVID), gene ontology (GO) tree machine, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis.

Results: There were totally 186 differentially expressed tags (P < 0.05, P(CK/AS)) between the libraries of CK and AS, 130 differentially expressed tags between libraries of AS/ASAC (P < 0.05, P(AS/ASAC)), and 144 differentially expressed tags between libraries of CK/CKAC (P < 0.05, P(CK/CKAC)). The gene expression profiles of AS and ASAC were more similar than other libraries via unsupervised SAGE clustering. By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC). Totally 3 same KEGG pathways were found among the three groups. Moreover, 21 specific tags of the acupuncture in treating asthma were detected using Venn diagrams.

Conclusion: Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

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The DAG graphs of the PCK/CKAC. 144 differentially expressed tags between libraries of CK and CKAC have matched 10 enriched GO categories of biological process by using the GO Tree Machine.
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Figure 7: The DAG graphs of the PCK/CKAC. 144 differentially expressed tags between libraries of CK and CKAC have matched 10 enriched GO categories of biological process by using the GO Tree Machine.

Mentions: There were 25, 5 and 10 enriched GO categories of biological process in PCK/AS, PAS/ASAC and PCK/CKAC respectively (Figure 5, 6, 7). Biosynthesis was only one overlapping GO term among them. The GO terms, such as antigen processing and presentation, cell migration, acetylcholine receptor signaling, muscarinic pathway disappeared in PAS/ASAC, and new GO terms, like regulation of biosynthesis, regulation of liquid surface tension, epidermal growth factor receptor signaling pathway appeared in PAS/ASAC when compared with PCK/AS. Regulation of liquid surface tension was the only shared GO term between PAS/ASAC and PCK/CKAC.


Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture.

Yin LM, Jiang GH, Wang Y, Wang Y, Liu YY, Jin WR, Xu YD, Zhang QH, Yang YQ - J. Biomed. Sci. (2009)

The DAG graphs of the PCK/CKAC. 144 differentially expressed tags between libraries of CK and CKAC have matched 10 enriched GO categories of biological process by using the GO Tree Machine.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698896&req=5

Figure 7: The DAG graphs of the PCK/CKAC. 144 differentially expressed tags between libraries of CK and CKAC have matched 10 enriched GO categories of biological process by using the GO Tree Machine.
Mentions: There were 25, 5 and 10 enriched GO categories of biological process in PCK/AS, PAS/ASAC and PCK/CKAC respectively (Figure 5, 6, 7). Biosynthesis was only one overlapping GO term among them. The GO terms, such as antigen processing and presentation, cell migration, acetylcholine receptor signaling, muscarinic pathway disappeared in PAS/ASAC, and new GO terms, like regulation of biosynthesis, regulation of liquid surface tension, epidermal growth factor receptor signaling pathway appeared in PAS/ASAC when compared with PCK/AS. Regulation of liquid surface tension was the only shared GO term between PAS/ASAC and PCK/CKAC.

Bottom Line: By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC).Totally 3 same KEGG pathways were found among the three groups.Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China. collegeylm@hotmail.com

ABSTRACT

Background: Asthma has become an important public health issue and approximately 300 million people have suffered from the disease worldwide. Nowadays, the use of acupuncture in asthma is increasing. This study intended to systematically analyze and compare the gene expression profiles between the asthmatic and acupuncture-treated asthmatic rat lung, and tried to gain insight into the molecular mechanism underlying the early airway response (EAR) phase of asthma treated by acupuncture.

Methods: Four tag libraries of serial analysis of gene expression (SAGE) were established from lung tissues of control rats (CK), asthmatic rats (AS), asthmatic rats treated by acupuncture (ASAC), and control rats treated by acupuncture (CKAC). Bioinformatic analyses were carried out by using the methods including unsupervised hierarchical clustering, functional annotation tool of the database for annotation, visualization, and integrated discovery (DAVID), gene ontology (GO) tree machine, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis.

Results: There were totally 186 differentially expressed tags (P < 0.05, P(CK/AS)) between the libraries of CK and AS, 130 differentially expressed tags between libraries of AS/ASAC (P < 0.05, P(AS/ASAC)), and 144 differentially expressed tags between libraries of CK/CKAC (P < 0.05, P(CK/CKAC)). The gene expression profiles of AS and ASAC were more similar than other libraries via unsupervised SAGE clustering. By comparison of P(CK/AS) and P(AS/ASAC), the DAVID genes functional classification was found to be changed from "immune response" to "response to steroid hormone stimulus", and the GO term "antigen processing and presentation of peptide antigen" disappeared in P(AS/ASAC). Totally 3 same KEGG pathways were found among the three groups. Moreover, 21 specific tags of the acupuncture in treating asthma were detected using Venn diagrams.

Conclusion: Our SAGE research indicates that the gene expression profile of the EAR phase of asthma could be effectively and specifically regulated by acupuncture, which suggests that the gene expression of immune response and steroid hormone may play an important role in the treatment.

Show MeSH
Related in: MedlinePlus